non-targeted-metabolomics-of-microbial-syncom-FDAT_release.zip
non-targeted-metabolomics-of-microbial-syncom-FDAT_release
.arc
.gitkeep
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.gitattributes
459 Bytes
LICENSE
18.7 kB
README.md
3.1 kB
assays
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UHPLC_MS_MS_measurements
README.md
2.0 kB
dataset
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Process_blanks_from_measurement
Blank_1.mzML
92.9 MB
Blank_1_20231027123936.mzML
92.2 MB
Blank_1_3.mzML
96.4 MB
Blank_2.mzML
91.8 MB
Blank_3.mzML
89.9 MB
Blank_out.mzML
93.3 MB
Blank_out_2.mzML
95.4 MB
Blank_start.mzML
110.2 MB
Blank_start_2.mzML
93.7 MB
Blank_start_4.mzML
98.4 MB
QC-mix_1.mzML
86.7 MB
QC-mix_1_1.mzML
86.1 MB
QC-mix_1_2.mzML
87.6 MB
QC-mix_2.mzML
89.1 MB
QC-mix_3.mzML
88.3 MB
QC-mix_out.mzML
89.9 MB
QC-mix_out_2.mzML
92.8 MB
QC-mix_start.mzML
89.1 MB
QC-mix_start_1.mzML
89.4 MB
QC-mix_start_2.mzML
95.3 MB
QC-mix_start_3.mzML
86.9 MB
QC-mix_start_4.mzML
93.3 MB
QCMix_1_3.mzML
87.7 MB
QCMix_1_4.mzML
90.0 MB
QCMix_1_5.mzML
82.2 MB
QCMix_1_6.mzML
93.2 MB
Single_strain_UHPLC_measurement
100.mzML
91.5 MB
101.mzML
90.5 MB
105_2.mzML
90.8 MB
107_2.mzML
90.7 MB
109.mzML
86.0 MB
10_20231027114858.mzML
90.9 MB
114_2.mzML
91.6 MB
115_2.mzML
90.7 MB
116_2.mzML
93.0 MB
11_20231027120551.mzML
91.6 MB
123.mzML
79.7 MB
125.mzML
79.9 MB
126.mzML
78.3 MB
19.mzML
90.7 MB
193_20231027095050.mzML
93.0 MB
194_20231027100743.mzML
91.8 MB
195_20231027102436.mzML
91.8 MB
196.mzML
94.8 MB
197.mzML
93.6 MB
198.mzML
93.0 MB
1_2_20231027104128.mzML
81.0 MB
20.mzML
92.3 MB
21.mzML
91.0 MB
25.mzML
91.3 MB
26.mzML
91.4 MB
27.mzML
88.6 MB
2_2_20231027105821.mzML
80.4 MB
33.mzML
87.1 MB
34.mzML
83.6 MB
35.mzML
87.2 MB
41.mzML
75.5 MB
42_20231029123225.mzML
98.5 MB
43.mzML
77.1 MB
49.mzML
89.2 MB
4_2_20231027111513.mzML
79.5 MB
50.mzML
89.0 MB
51.mzML
90.2 MB
57.mzML
93.0 MB
58.mzML
94.3 MB
59.mzML
93.0 MB
67.mzML
87.6 MB
68.mzML
87.4 MB
69.mzML
87.2 MB
73.mzML
91.7 MB
74.mzML
92.7 MB
75.mzML
90.1 MB
81.mzML
91.5 MB
82.mzML
91.5 MB
83.mzML
91.5 MB
90.mzML
90.2 MB
91.mzML
87.6 MB
92.mzML
87.1 MB
99.mzML
91.0 MB
9_20231027113206.mzML
87.3 MB
Standards_UHPLC_measurement
biotin.mzML
93.1 MB
biotin.raw
264.0 MB
isopentenyl_adenosine.mzML
96.8 MB
isopentenyl_adenosine.raw
289.1 MB
trans_zeatin.mzML
92.4 MB
trans_zeatin.raw
264.7 MB
trans_zeatin_ribosine.mzML
95.3 MB
trans_zeatin_ribosine.raw
277.8 MB
SynCom_co_culture_UHPLC_measure
148_2.mzML
79.8 MB
149_2.mzML
84.8 MB
150_2.mzML
88.4 MB
isa.assay.xlsx
33.3 kB
protocols
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UHPLC_measurement.docx
14.6 kB
UHPLC_measurement.pdf
80.1 kB
~$PLC measurements.docx
162 Bytes
isa.investigation.xlsx
11.7 kB
runs
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Feature_based_molecular_networking_single_and_SynCom
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GNPS2_FBMN_output
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featuretable_reformated.csv
5.4 MB
flow_filelinking.yaml
5.0 kB
job_dag.html
9.0 kB
job_parameters.yaml
1.4 kB
job_report.html
3.1 MB
job_timeline.html
295.0 kB
network_output
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Filesummary
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summaryresult.tsv
1 Byte
clustering
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featuretable_reformated.csv
5.4 MB
specs_ms.mgf
7.8 MB
spectra_filtered.mgf
8.2 MB
spectra_reformatted.mgf
8.2 MB
library
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merged_results_with_gnps.tsv
3.5 MB
merged_results_with_gnps.xlsx
1.6 MB
library_intermediate
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merged_results.tsv
1.4 MB
metadata
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merged_metadata.tsv
5.0 kB
networking
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clustersummary_with_groups.tsv
5.8 MB
clustersummary_with_network.tsv
6.1 MB
filtered_pairs.tsv
418.4 kB
merged_pairs.tsv
16.6 MB
network.graphml
25.8 MB
network_singletons.graphml
39.4 MB
params
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0.params
176 Bytes
1.params
179 Bytes
10.params
181 Bytes
11.params
181 Bytes
2.params
179 Bytes
3.params
179 Bytes
4.params
179 Bytes
5.params
180 Bytes
6.params
181 Bytes
7.params
181 Bytes
8.params
181 Bytes
9.params
181 Bytes
temp_pairs
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0.params_aligns.tsv
445.7 kB
1.params_aligns.tsv
698.4 kB
10.params_aligns.tsv
1.2 MB
11.params_aligns.tsv
566.4 kB
2.params_aligns.tsv
896.0 kB
3.params_aligns.tsv
695.2 kB
4.params_aligns.tsv
538.5 kB
5.params_aligns.tsv
325.8 kB
6.params_aligns.tsv
944.0 kB
7.params_aligns.tsv
2.4 MB
8.params_aligns.tsv
5.1 MB
9.params_aligns.tsv
2.7 MB
nextflow_stdout.log
99.8 kB
nf_cmd.sh
641 Bytes
nf_resume_cmd.sh
649 Bytes
submission_parameters.yaml
920 Bytes
workflowdisplay.yaml
10.5 kB
MZmine3_output
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MZmine_output_for_GNPS.mgf
7.8 MB
MZmine_output_for_GNPS_quant.csv
3.5 MB
MZmine_output_for_SIRIUS.mgf
16.9 MB
SIRIUS_output
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canopus_compound_summary.tsv
9.4 MB
canopus_formula_summary.csv
9.4 MB
canopus_formula_summary_adducts.tsv
9.7 MB
compound_identifications.tsv
3.6 MB
compound_identifications_adducts.tsv
3.8 MB
formula_identifications.tsv
2.2 MB
formula_identifications_adducts.tsv
2.3 MB
predictions.tsv
781.7 MB
report.mztab
11.3 MB
fbmn_statsguide_statistical_analysis
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ANOVA_significance_table.csv
847.3 kB
PCA_all.svg
35.7 kB
PCA_and_PCoA_single_and_SynCom.pptx
299.6 kB
PCA_and_PCoA_single_and_SynCom.svg
24.4 kB
PCoA_all.svg
36.0 kB
principal-component-analysis.svg
33.3 kB
principal-coordinate-analysis (1).svg
35.0 kB
principal-coordinate-analysis_syncom.svg
20.3 kB
isa.runs.xlsx
24.5 kB
metadata_single_and_SynCom_for_GNPS2.xlsx
12.5 kB
externat_supplements_manuscript
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Batch_mode_for_Mzmine3.xml
22.9 kB
Feature_based_molecula_network_single_strains_and_syncom_co_cultures.cys
4.6 MB
Table_ES1_GNPS2_annotated_compounds_and_their_producers.xlsm
125.8 kB
prokka_annotated_genomes
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Aeromicrobium_sp_200-1B3.gbk
7.8 MB
Arthrobacter_sp_53_contigs.gbk
10.6 MB
Bacillus_sp_63.gbk
8.6 MB
Flavobacterium_sp_9.gbk
10.1 MB
Frigobacterium_sp_200.1B2.gbk
6.8 MB
Massilia_sp._contigs(1).gbk
11.9 MB
Methylobacterium_sp.Leaf104.gbk
10.1 MB
Microbacterium_proteolyticum.gbk
7.2 MB
Nocardioides.gbk
9.5 MB
Paenibacillus_taichungensis.gbk
14.6 MB
Pseudomonas_sp_3.2.gbk
14.1 MB
Rhizobium_sp_24.gbk
10.6 MB
Sphingomonas_faeni_ERG1.4.gbk
8.2 MB
polished_assembly_Dioszegia EY.gbk
46.1 MB
table_ES2_annotated_N_acyl_amino_acids.xlsx
16.3 kB
table_ES3_compound_class_predictions_SIRIUS.xlsx
2.3 MB
table_ES4_quant_table_after_fbmn_processing.xlsx
2.3 MB
table_ES5_ANOVA_significance_table.xlsx
249.3 kB
table_ES6_final_table_of_significant_metabolites_in_syncom.xlsx
130.5 kB
studies
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UHPLC_MS_MS_single_and_SynCom
README.md
1.2 kB
isa.study.xlsx
33.8 kB
protocols
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MM9_7_Agar.docx
14.6 kB
MM9_7_Agar.pdf
139.7 kB
Protocol for UHPLC_MS_MS sample preparation.docx
14.0 kB
Protocol for UHPLC_MS_MS sample preparation.pdf
74.4 kB
~$9_7_Agar.docx
162 Bytes
resources
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ARC.jpg
1.4 MB
workflows
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Batch_mode_for_Mzmine3.xml
23.2 kB
Protocol Statistical analysis.docx
13.8 kB
Protocol Statistical analysis.pdf
120.2 kB
Protocol data processing.docx
13.9 kB
Protocol data processing.pdf
98.1 kB
Protocol for GNPS2 and SIRIUS analysis.docx
14.0 kB
Protocol for GNPS2 and SIRIUS analysis.pdf
90.3 kB
~$otocol data processing.docx
162 Bytes